# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:47:24 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccnc1[C@H](NC[C@H]2O[C@H](C[C@@H]2O)N3C=CC(=O)NC3=O)c4ccccc4
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 DU2  DU2  2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine  ligand  52  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DU2
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 DU2  N1    N  NR6   0  -0.567  -3.0564  -0.5016   0.4359
 DU2  C2    C  CR6   0   0.736  -4.4084  -0.3333   0.6358
 DU2  O2    O  O     0  -0.484  -5.1711  -1.2704   0.7664
 DU2  N3    N  NR16  0  -0.730  -4.8335   0.9676   0.6749
 DU2  C4    C  CR6   0   0.565  -4.0617   2.1165   0.5793
 DU2  O4    O  O     0  -0.470  -4.5828   3.2169   0.6248
 DU2  C5    C  CR16  0  -0.522  -2.6559   1.8428   0.4436
 DU2  C6    C  CR16  0   0.066  -2.2180   0.5711   0.3875
 DU2  C1'   C  CH1   0   0.198  -2.5669  -1.9088   0.3619
 DU2  C17   C  CH1   0  -0.217   2.5239  -0.2132  -0.6794
 DU2  C18   C  CR6   0   0.113   3.6699  -0.3800   0.2985
 DU2  C19   C  CR16  0  -0.327   4.9392  -0.7293  -0.1450
 DU2  C2'   C  CH2   0  -0.539  -2.9869  -2.6032  -0.9255
 DU2  C20   C  CR16  0  -0.242   5.9842  -0.8895   0.7587
 DU2  C21   C  CR16  0  -0.265   5.7617  -0.7060   2.1152
 DU2  C22   C  CR16  0  -0.242   4.4914  -0.3602   2.5653
 DU2  C23   C  CR16  0  -0.270   3.4524  -0.1963   1.6627
 DU2  C24   C  CR5   0   0.494   2.0215   1.2026  -0.6272
 DU2  N25   N  N     0  -0.445   1.0071   1.6417   0.0774
 DU2  C26   C  CR15  0  -0.222   0.9747   2.9922  -0.1208
 DU2  C27   C  CR15  0  -0.119   1.9838   3.3684  -0.9563
 DU2  N28   N  NR5   0  -0.443   2.6438   2.2147  -1.2787
 DU2  C29   C  CH3   0  -0.536   3.8217   2.1271  -2.1141
 DU2  C3'   C  CH1   0   0.019  -1.8448  -2.2493  -1.8702
 DU2  C4'   C  CH1   0   0.005  -0.6457  -2.2271  -0.9239
 DU2  O4'   O  O2    0  -0.488  -1.1790  -1.9084   0.3651
 DU2  O41   O  OH1   0  -0.663  -1.6154  -3.1621  -2.9074
 DU2  C5'   C  CH2   0  -0.282   0.4197  -1.2330  -1.3349
 DU2  N5'   N  NH1   0  -0.584   1.4686  -1.1449  -0.3413
 DU2  HN3   H  HNR6  0   0.424  -5.8309   1.0921   0.7988
 DU2  H5    H  HCR6  0   0.286  -1.9541   2.6604   0.3966
 DU2  H6    H  HCR6  0   0.348  -1.1570   0.3702   0.3207
 DU2  H1'   H  HCH1  0   0.280  -2.9337  -2.4137   1.2562
 DU2  H17   H  HCH1  0   0.244   2.9213  -0.3969  -1.6924
 DU2  H19   H  HCR6  0   0.253   5.1150  -0.8824  -1.2035
 DU2  H2'   H  HCH2  0   0.264  -2.9970  -3.6820  -0.7513
 DU2  H2'A  H  HCH2  0   0.279  -3.9683  -2.3117  -1.2924
 DU2  H20   H  HCR6  0   0.256   6.9684  -1.1612   0.4002
 DU2  H21   H  HCR6  0   0.256   6.5720  -0.8314   2.8217
 DU2  H22   H  HCR6  0   0.255   4.3128  -0.2171   3.6233
 DU2  H23   H  HCR6  0   0.253   2.4660   0.0824   2.0121
 DU2  H26   H  HCR5  0   0.247   0.2300   3.6207   0.3426
 DU2  H27   H  HCR5  0   0.286   2.2814   4.3268  -1.3482
 DU2  H29   H  HCH3  0   0.260   3.7392   1.2908  -2.8045
 DU2  H29A  H  HCH3  0   0.273   3.9131   3.0410  -2.6940
 DU2  H29B  H  HCH3  0   0.260   4.7220   2.0016  -1.5140
 DU2  H3'   H  HCH1  0   0.221  -2.0067  -1.2382  -2.2702
 DU2  H4'   H  HCH1  0   0.242  -0.2117  -3.2347  -0.8699
 DU2  HO41  H  HOH1  0   0.461  -2.2878  -3.0302  -3.5825
 DU2  H5'   H  HCH2  0   0.226   0.7867  -1.5374  -2.3281
 DU2  H5'A  H  HCH2  0   0.230  -0.0339  -0.2472  -1.4635
 DU2  HN5'  H  HNH1  0   0.354   1.8886  -2.0591  -0.2181

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 DU2  N1   C2    single    1.377  0.020  1.377
 DU2  N1   C6    single    1.362  0.020  1.362
 DU2  N1   C1'   single    1.492  0.020  1.492
 DU2  C2   O2    double    1.215  0.020  1.215
 DU2  C2   N3    single    1.369  0.020  1.369
 DU2  N3   C4    single    1.387  0.020  1.387
 DU2  C4   O4    double    1.218  0.020  1.218
 DU2  C4   C5    single    1.439  0.020  1.439
 DU2  C5   C6    double    1.346  0.020  1.346
 DU2  C1'  C2'   single    1.522  0.020  1.522
 DU2  C1'  O4'   single    1.388  0.020  1.388
 DU2  C17  C18   single    1.516  0.020  1.516
 DU2  C17  C24   single    1.503  0.020  1.503
 DU2  C17  N5'   single    1.448  0.020  1.448
 DU2  C18  C19   aromatic  1.389  0.020  1.389
 DU2  C18  C23   aromatic  1.394  0.020  1.394
 DU2  C19  C20   aromatic  1.391  0.020  1.391
 DU2  C2'  C3'   single    1.524  0.020  1.524
 DU2  C20  C21   aromatic  1.387  0.020  1.387
 DU2  C21  C22   aromatic  1.391  0.020  1.391
 DU2  C22  C23   aromatic  1.386  0.020  1.386
 DU2  C24  N25   aromatic  1.311  0.020  1.311
 DU2  C24  N28   aromatic  1.355  0.020  1.355
 DU2  N25  C26   aromatic  1.365  0.020  1.365
 DU2  C26  C27   aromatic  1.363  0.020  1.363
 DU2  C27  N28   aromatic  1.368  0.020  1.368
 DU2  N28  C29   single    1.447  0.020  1.447
 DU2  C3'  C4'   single    1.528  0.020  1.528
 DU2  C3'  O41   single    1.401  0.020  1.401
 DU2  C4'  O4'   single    1.431  0.020  1.431
 DU2  C4'  C5'   single    1.514  0.020  1.514
 DU2  C5'  N5'   single    1.447  0.020  1.447
 DU2  N3   HN3   single    0.860  0.020  1.020
 DU2  C5   H5    single    0.930  0.020  1.080
 DU2  C6   H6    single    0.930  0.020  1.080
 DU2  C1'  H1'   single    0.970  0.020  1.090
 DU2  C17  H17   single    0.970  0.020  1.090
 DU2  C19  H19   single    0.930  0.020  1.080
 DU2  C2'  H2'   single    0.970  0.020  1.090
 DU2  C2'  H2'A  single    0.970  0.020  1.090
 DU2  C20  H20   single    0.930  0.020  1.080
 DU2  C21  H21   single    0.930  0.020  1.080
 DU2  C22  H22   single    0.930  0.020  1.080
 DU2  C23  H23   single    0.930  0.020  1.080
 DU2  C26  H26   single    0.930  0.020  1.080
 DU2  C27  H27   single    0.930  0.020  1.080
 DU2  C29  H29   single    0.970  0.020  1.090
 DU2  C29  H29A  single    0.970  0.020  1.090
 DU2  C29  H29B  single    0.970  0.020  1.090
 DU2  C3'  H3'   single    0.970  0.020  1.090
 DU2  C4'  H4'   single    0.970  0.020  1.090
 DU2  O41  HO41  single    0.850  0.020  0.980
 DU2  C5'  H5'   single    0.970  0.020  1.090
 DU2  C5'  H5'A  single    0.970  0.020  1.090
 DU2  N5'  HN5'  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 DU2  C1'   N1   C6    122.62  3.000
 DU2  C1'   N1   C2    116.40  3.000
 DU2  C6    N1   C2    120.88  3.000
 DU2  N3    C2   O2    122.32  3.000
 DU2  N3    C2   N1    115.16  3.000
 DU2  O2    C2   N1    122.52  3.000
 DU2  HN3   N3   C4    117.03  3.000
 DU2  HN3   N3   C2    115.22  3.000
 DU2  C4    N3   C2    127.74  3.000
 DU2  C5    C4   O4    126.38  3.000
 DU2  C5    C4   N3    113.12  3.000
 DU2  O4    C4   N3    120.49  3.000
 DU2  H5    C5   C6    120.17  3.000
 DU2  H5    C5   C4    119.72  3.000
 DU2  C6    C5   C4    120.10  3.000
 DU2  H6    C6   C5    119.81  3.000
 DU2  H6    C6   N1    117.35  3.000
 DU2  C5    C6   N1    122.83  3.000
 DU2  H1'   C1'  O4'   109.55  3.000
 DU2  H1'   C1'  C2'   112.93  3.000
 DU2  O4'   C1'  C2'   106.15  3.000
 DU2  H1'   C1'  N1    106.60  3.000
 DU2  O4'   C1'  N1    109.13  3.000
 DU2  C2'   C1'  N1    112.45  3.000
 DU2  H17   C17  N5'   111.70  3.000
 DU2  H17   C17  C24   108.00  3.000
 DU2  N5'   C17  C24   110.75  3.000
 DU2  H17   C17  C18   107.56  3.000
 DU2  N5'   C17  C18   109.25  3.000
 DU2  C24   C17  C18   109.51  3.000
 DU2  C23   C18  C19   119.23  3.000
 DU2  C23   C18  C17   119.94  3.000
 DU2  C19   C18  C17   120.83  3.000
 DU2  H19   C19  C20   119.76  3.000
 DU2  H19   C19  C18   119.71  3.000
 DU2  C20   C19  C18   120.53  3.000
 DU2  H2'A  C2'  H2'   108.06  3.000
 DU2  H2'A  C2'  C3'   113.88  3.000
 DU2  H2'   C2'  C3'   109.57  3.000
 DU2  H2'A  C2'  C1'   114.34  3.000
 DU2  H2'   C2'  C1'   108.56  3.000
 DU2  C3'   C2'  C1'   102.22  3.000
 DU2  H20   C20  C21   120.21  3.000
 DU2  H20   C20  C19   119.80  3.000
 DU2  C21   C20  C19   119.99  3.000
 DU2  H21   C21  C22   120.08  3.000
 DU2  H21   C21  C20   120.20  3.000
 DU2  C22   C21  C20   119.72  3.000
 DU2  H22   C22  C23   119.81  3.000
 DU2  H22   C22  C21   119.98  3.000
 DU2  C23   C22  C21   120.21  3.000
 DU2  H23   C23  C22   120.21  3.000
 DU2  H23   C23  C18   119.47  3.000
 DU2  C22   C23  C18   120.32  3.000
 DU2  N28   C24  N25   111.32  3.000
 DU2  N28   C24  C17   122.23  3.000
 DU2  N25   C24  C17   126.36  3.000
 DU2  C26   N25  C24   105.76  3.000
 DU2  H26   C26  C27   127.83  3.000
 DU2  H26   C26  N25   122.02  3.000
 DU2  C27   C26  N25   110.15  3.000
 DU2  H27   C27  N28   122.09  3.000
 DU2  H27   C27  C26   132.30  3.000
 DU2  N28   C27  C26   105.60  3.000
 DU2  C29   N28  C27   125.46  3.000
 DU2  C29   N28  C24   127.32  3.000
 DU2  C27   N28  C24   107.17  3.000
 DU2  H29B  C29  H29A  108.75  3.000
 DU2  H29B  C29  H29   108.90  3.000
 DU2  H29A  C29  H29   108.33  3.000
 DU2  H29B  C29  N28   111.21  3.000
 DU2  H29A  C29  N28   109.01  3.000
 DU2  H29   C29  N28   110.57  3.000
 DU2  H3'   C3'  O41   110.73  3.000
 DU2  H3'   C3'  C4'   109.12  3.000
 DU2  O41   C3'  C4'   109.85  3.000
 DU2  H3'   C3'  C2'   109.20  3.000
 DU2  O41   C3'  C2'   115.50  3.000
 DU2  C4'   C3'  C2'   101.99  3.000
 DU2  H4'   C4'  C5'   109.73  3.000
 DU2  H4'   C4'  O4'   107.90  3.000
 DU2  C5'   C4'  O4'   111.13  3.000
 DU2  H4'   C4'  C3'   109.11  3.000
 DU2  C5'   C4'  C3'   113.19  3.000
 DU2  O4'   C4'  C3'   105.59  3.000
 DU2  C4'   O4'  C1'   111.75  3.000
 DU2  HO41  O41  C3'   108.41  3.000
 DU2  H5'A  C5'  H5'   106.34  3.000
 DU2  H5'A  C5'  N5'   109.07  3.000
 DU2  H5'   C5'  N5'   113.22  3.000
 DU2  H5'A  C5'  C4'   109.40  3.000
 DU2  H5'   C5'  C4'   107.32  3.000
 DU2  N5'   C5'  C4'   111.32  3.000
 DU2  HN5'  N5'  C5'   109.19  3.000
 DU2  HN5'  N5'  C17   107.86  3.000
 DU2  C5'   N5'  C17   114.02  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 DU2  CONST_01  C21  C20  C19  C18    0.00   0.0  0
 DU2  CONST_02  C21  C22  C23  C18    0.00   0.0  0
 DU2  CONST_03  C22  C23  C18  C19    0.00   0.0  0
 DU2  CONST_04  C22  C21  C20  C19    0.00   0.0  0
 DU2  CONST_05  C23  C18  C19  C20    0.00   0.0  0
 DU2  CONST_06  C23  C22  C21  C20    0.00   0.0  0
 DU2  CONST_07  C27  C26  N25  C24    0.00   0.0  0
 DU2  CONST_08  C26  C27  N28  C24    0.00   0.0  0
 DU2  CONST_09  C27  N28  C24  N25    0.00   0.0  0
 DU2  CONST_10  N28  C27  C26  N25    0.00   0.0  0
 DU2  CONST_11  N28  C24  N25  C26    0.00   0.0  0
 DU2  CONST_12  C4   N3   C2   N1     0.00   0.0  0
 DU2  CONST_13  C5   C4   N3   C2     0.00   0.0  0
 DU2  CONST_14  C6   N1   C2   N3     0.00   0.0  0
 DU2  CONST_15  C1'  N1   C2   N3   180.00   0.0  0
 DU2  CONST_16  C20  C19  C18  C17  180.00   0.0  0
 DU2  CONST_17  C22  C23  C18  C17  180.00   0.0  0
 DU2  CONST_18  C26  N25  C24  C17  180.00   0.0  0
 DU2  CONST_19  C27  N28  C24  C17  180.00   0.0  0
 DU2  CONST_20  C29  N28  C24  N25  180.00   0.0  0
 DU2  CONST_21  C29  N28  C27  C26  180.00   0.0  0
 DU2  CONST_22  O4   C4   N3   C2   180.00   0.0  0
 DU2  CONST_23  C6   N1   C2   O2   180.00   0.0  0
 DU2  CONST_24  C1'  N1   C2   O2     0.00   0.0  0
 DU2  CONST_25  C4   N3   C2   O2   180.00   0.0  0
 DU2  CONST_26  H20  C20  C19  C18  180.00   0.0  0
 DU2  CONST_27  H22  C22  C23  C18  180.00   0.0  0
 DU2  CONST_28  H23  C23  C18  C19  180.00   0.0  0
 DU2  CONST_29  H21  C21  C20  C19  180.00   0.0  0
 DU2  CONST_30  H19  C19  C20  C21  180.00   0.0  0
 DU2  CONST_31  H26  C26  N25  C24  180.00   0.0  0
 DU2  CONST_32  H27  C27  N28  C24  180.00   0.0  0
 DU2  CONST_33  HN3  N3   C2   N1   180.00   0.0  0
 DU2  Var_01    H29  C29  N28  C24   46.02  30.0  2
 DU2  Var_02    C4'  C5'  N5'  C17  179.71  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 DU2  chir_01  C1'  N1   C2'  O4'  negativ
 DU2  chir_02  C17  N5'  C18  C24  positiv
 DU2  chir_03  C3'  O41  C2'  C4'  negativ
 DU2  chir_04  C4'  O4'  C3'  C5'  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 DU2  plan-1  C17  0.020
 DU2  plan-1  C24  0.020
 DU2  plan-1  N25  0.020
 DU2  plan-1  C26  0.020
 DU2  plan-1  C27  0.020
 DU2  plan-1  N28  0.020
 DU2  plan-1  C29  0.020
 DU2  plan-1  H26  0.020
 DU2  plan-1  H27  0.020
 DU2  plan-2  N1   0.020
 DU2  plan-2  C2   0.020
 DU2  plan-2  O2   0.020
 DU2  plan-2  N3   0.020
 DU2  plan-2  C4   0.020
 DU2  plan-2  O4   0.020
 DU2  plan-2  C5   0.020
 DU2  plan-2  C6   0.020
 DU2  plan-2  C1'  0.020
 DU2  plan-2  HN3  0.020
 DU2  plan-2  H5   0.020
 DU2  plan-2  H6   0.020
 DU2  plan-3  C17  0.020
 DU2  plan-3  C18  0.020
 DU2  plan-3  C19  0.020
 DU2  plan-3  C20  0.020
 DU2  plan-3  C21  0.020
 DU2  plan-3  C22  0.020
 DU2  plan-3  C23  0.020
 DU2  plan-3  H19  0.020
 DU2  plan-3  H20  0.020
 DU2  plan-3  H21  0.020
 DU2  plan-3  H22  0.020
 DU2  plan-3  H23  0.020

